• Preface
• HTML documents
• R Code Chunks
• Markdown Basics
• R Presentation
• ioslides
• Miscellaneous

• Markdown
  • Remove HTML tag for higher readibility.
  • Inline HTML is avaliable.
• R markdown
  • Markdown + embedded R code chunks
  • Rmd -> md -> html(docx, pdf)
  • Literate Programming

• v1: based on package knitr and markdown
• v2: based on knitr and pandoc, intergrated into RStudio v0.98.932 or later
  • default bootstrap template
  • docx and pdf
  • slides with ioslides and Beamer
  • embedded shiny apps
• keep using R Markdown v1

<-- rmarkdown v1 -->

• RStudio — Install the latest version of RStudio

• Other environments — Install the rmarkdown package.

• YAML Metadata: YAML document options
• Markdown: Article text
• R Code Chunk: Executible R code

• RStudio: "Knit" command (Ctrl+Shift+K)

• Command line: rmarkdown::render function

  rmarkdown::render("input.Rmd")

With Rstudio, You can edit various output options with friendly UI.

---
title: "R Markdown Exercise"
author: "Mansun Kuo"
date: "July 24, 2014"
output:
  html_document:
    css: assets/css/custom.css
    fig_caption: no
    fig_height: 5
    fig_width: 7
    highlight: default
    keep_md: no
    number_sections: no
    theme: default
    toc: yes
---

CSS:

#nextsteps {
   color: blue;
}

.emphasized {
   font-size: 1.2em;
}

Apply to Whole Section:

### Apply to Whole Section {#nextsteps .emphasized}

使用RStudio產生一個HTML文件:

• 標題為油電業薪資近9萬，是教服業的4倍?。

• include table of contents

*italic*   **bold**

_italic_   __bold__

I am italic

I am bold

Setext:

Header 1
=============

Header 2
-------------

atx:

# Header 1

## Header 2

### Header 3

End a line with two or more spaces:

Roses are red,  
Violets are blue.

Subsequent paragraphs must be preceded by a blank line and indented four spaces or a tab.

* fruits

    delicious!!!
    + apples
        - macintosh
        - red delicious
    + pears
    + peaches
* vegetables  
  healthy!!!
    + broccoli
    + chard

R code will be evaluated and printed

```{r}
summary(cars$dist)
```

summary(cars$dist)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##       2      26      36      43      56     120

I counted 2 red trucks on the highway.

A plain http address or add a link to a phrase.

Inline Link:

[2014台灣資料科學愛好者年會](http://twconf.data-sci.org/)

2014台灣資料科學愛好者年會

Reference Link:

[2014台灣資料科學愛好者年會][dsc]
[dsc]: http://twconf.data-sci.org/

2014台灣資料科學愛好者年會

A friend once said:

> It's always better to give
> than to receive.

• Plain code blocks are displayed in a fixed-width font but not evaulated.

  ```
  This text is displayed verbatim / preformatted
  ```
  

• Specify the language of the block is avaliable

  ```r
  x = rnorm(10)
  ```

  x = rnorm(10)

• LaTeX
  • Inline equation: $equation$
    

  • Display equation: $$ equation $$

  • Useful Resources
    • Daum Equation Editor: Chrome Plugin
    • Online LaTeX Equation Editor
• MathML
  • <math ...> </math> for equations.

Three or more asterisks or dashes:

******

------

加上報告的段落標題

• 每人每月薪資 - Top 3 & Last 3

• 行業別每人每月薪資總表

• Named R code chunk.

  ```{r plot}
  summary(cars)
  plot(cars)
  ```
  

• Easy Navigation in RStudio

  

• echo(TRUE): whether to include R source code in the output file
• eval(TRUE): whether to evaluate the code chunk
• message(TRUE): whether to preserve messages emitted by message()
• include(TRUE): if include=FALSE, nothing will be written into the output document, but the code is still evaluated and plot files are generated
• warning(TRUE): whether to preserve warnings in the output

```{r plot, include=FALSE}
# Disable all output 
```

```{r plot, echo=FALSE}
# Hide source code
```

• dev('png'): figure format(png, jpeg, tiff, svg, …)
• fig.path('figure/'): figure path
• fig.width(7): figure width
• fig.height(7): figure height
• dpi(72): DPI (dots per inch)

```{r dev='svg', fig.path='myplot', fig.height=8}
plot(iris)
```

Set results='asis' to write raw results from R into the output document

• cache(FALSE): whether to cache a code chunk to improve proformance for expensive computing

• Caching globally for a document

```{r setup, include=FALSE}
knitr::opts_chunk$set(cache=TRUE)
```

• If you run into problems with cached output, you can always clear the knitr cache by removing the folder named with a _cache suffix.

• engine('R'): the language name of the code chunk
  • 'bash'
  • 'python'
  • 'Rcpp'

```{r engine='bash'}
whoami
```

結合適當的圖表和文字敘述， 將從每人每月平均薪資和消費者物價指數資料中觀察到的現象完成一份完整的報告。

• 報告範例
• Rmd File
• 主題
  • 油電業薪資近9萬，是教服業的4倍？
  • 實質薪資倒退十五年？
• 小提示
  • 利用knitr::opts_chunk$set將整份報告的warning設為FALSE 來處理中文問題
  • 繪製"油電業薪資近9萬，是教服業的4倍？"時， 設定dpi=75, fig.width=10
  • 試著隱藏source code

There are various way to publish your document on the web.

• RPubs
  • RPubs
  • markdown::rpubsUpload
• file hosting service
  • Dropbox
  • Google Drive

Deploy your slides on the web.

• A feature of RStudio that enable easy authoring of HTML5 presentations based on R Markdown.
• Special Feature
  • Extensive support for authoring and previewing presentations within the RStudio IDE
  • Flexible two column layouts
• Getting Started

Set global option in first slide.

R Presentation
========================================================
author: Mansun Kuo
date: June 22, 2014

Slides automatically display their titles unless title: false is specified.

Slide 1
====================================
title: false

- Bullet 1
- Bullet 2
- Bullet 3

• Every time you save your presentation the preview is refreshed and navigated to whatever slide you were editing.
• Within the preview pane, you can press the Edit button on the toolbar to jump immediately to it's location in the source file.

Two-Column Slide
====================================
left: 70%

First column
***
Second column

• transition: transition style
  • none, linear, rotate, fade, zoom, concave
• transition-speed: transition speed
  • default, slow, fast

R Presentation
========================================================
author: Mansun Kuo
date: June 22, 2014
transition: rotate
transition-speed: fast

• type: slide appearance
  • section, sub-section, prompt, alert

Type
========================================================
type: sub-section
incremental: true

• incremental: display content incrementally
  • true, false

Incremental Display
========================================================
incremental: true

- Bullet 1
- Bullet 2
- Bullet 3

• Clear Knitr Cache: clear knitr cache for this presentation
• View in Browser: view the presentation in an external web browser
• Save AS Web Page: save the presentation as a standalone web page
• Publish to RPubs: publish the presentation to RPubs

R Presentation
========================================================
author: Mansun Kuo
date: June 22, 2014
css: assets/css/rpres.css

Apply to individual slides:

My Slide
===================================
class: illustration

Apply to spans of text:

My Slide
================================== 
<span class="emphasized">Pay attention to this!</span>

建立一個R Presentation

• A feature of RStudio that create an ioslides presentation.
• Special Feature
  • Code Highlighting
  • Presenter mode
• Getting Started

• #: create a section
• ##: create a new slide
• ---: create a new slide without a header(horizontal rule)
• |: add a subtitle

# section

## slide 1

---

## slide 2 | with subtitle

• 'f' enable fullscreen mode

• 'w' toggle widescreen mode

• 'o' enable overview mode

• 'h' enable code highlight mode

• 'p' show presenter notes

• 'Esc' exits all of these modes.

---
output:
  ioslides_presentation:
    incremental: true
---

Render bullets incrementally for specific slide:

> - Eat eggs
> - Drink coffee

• Eat eggs
• Drink coffee

• widescreen: widescreen mode
• smaller: smaller text

---
output:
  ioslides_presentation:
    widescreen: true
    smaller: true
---

Set smaller text for specific slide:

## Getting up {.smaller}

transition: default, slower, faster

---
output:
  ioslides_presentation:
    transition: slower
---

Add a 128x128 logo:

---
output:
  ioslides_presentation:
    logo: logo.png
---

Using ### <b> and ### </b> to enclose the lines you want to highlight.

x <- 10
y <- 20

Note that the content will flow across the columns.

<div class="columns-2">
  ![Image](assets/img/Taiwan-R-logo.png)

  - Bullet 1
  - Bullet 2
  - Bullet 3
</div>

You can color content using base color classes red, blue, green, yellow, and gray (or variations of them e.g. red2, red3, blue2, blue3, etc.).

<div class="red2">
This text is red
</div>

• red red2 red3
• blue blue2 blue3
• green green2 green3
• yellow yellow2 yellow3
• gray gray2 gray3

mypresentation.html?presentme=true

mypresentation.html?presentme=false

To add presenter notes:

<div class="notes">
This is my note.
- It can contain markdown
- like this list
</div>

建立一個ioslides

It’s possible to embed a Shiny application within a document.

You can add R Markdown and HTML in the YAML content.

```{r results='asis', echo=FALSE}
library(whisker)
temp = '<span class="{{color}}{{number}}">{{color}}{{number}}</span>'
numbers = c("", "2", "3")
colors = c("red", "blue", "green", "yellow", "gray")
for (color in colors){
    cat("- ")
    for (number in numbers){
        out = whisker.render(temp)
        cat(out)
    }
    cat("\n")
}
```

• iframe: 鑲嵌其他網頁

  <iframe src="http://twconf.data-sci.org/" height=600 width=800></iframe>

• img: 插入圖片，較容易調整長寬

  <img src="assets/img/Taiwan-R-logo.png" alt="logo" height="42" width="42">

library(knitr)
library(ggvis)
mtcars %>%
    ggvis(x = ~wt, y = ~mpg) %>%
    layer_smooths(se=TRUE, opacity := 0.5, opacity.hover := 0.75) %>% 
    layer_points(fill = ~factor(cyl), size := 50, size.hover := 200) %>%
    set_options(hover_duration = 250)

• R Markdown Cheat Sheet
• R Markdown
• knitr
• RStudio Documentation
• Reproducible Research
• Shiny Articles
• Slides GitHub Page
• googleVis簡介